AMBER Archive (2009)

Subject: [AMBER] PMEMD error message

From: neville forlemu (neville_forlemu_at_yahoo.com)
Date: Tue Mar 10 2009 - 09:55:31 CDT

hello,
I get this error message about my the following input file I modified from the amber advanced tutorials 3 section 1 on MM-PBSA.

annealing solvated joxfact complex
 &cntrl
 imin=0,irest=0,ntx=1,
 nstlim=50000,dt=0.002,
 ntc=2,ntf=2,
 cut=12.0,ntb=1,
 ntpr=500,ntwx=500,
 ntt=3,gamma_ln=2.0,
 tempi=0.0,temp0=300.00,
 ntr=1,
 nmropt=1
/
500
res 1 50000
&wt TYPE='TEMP0',istep1=0,istep2=25000,
 value1=0.1,value2=300.0,/
&wt TYPE='END'/

When I run the following command
mpirun -np 4 /opt/brinsoft/amber8/exe/pmemd -O -i heat.in -o heat.out -p joxfact_wat.top -c joxfact_watmin.rst -r heat.rst -x heat.mdcrd -ref joxfact_watmin.rst

lib-4001 : UNRECOVERABLE library error

Encountered during a sequential formatted READ from unit 5
Fortran unit 5 is connected to a sequential formatted text file: "heat.in"
 Current format:  9208 FORMAT(20a4)9018(/5x, 'GROUP', i5, ' HAS HARMONIC CONSTRAINTS', f12.5)127(' ', 5x, '***PROBLEMS WITH GROUP       ', a4, 14i5, '*******', /)222(' ', 5x, 'Number of atoms in this group  = ', i5)52(' ', 34x, i5, 2x, 'TO', i5)51(' ', 5x, 'GROUP',        i5, 3x, 'CONSISTS OF ATOMS -', /)46(' ', 5x, 'GROUP', i5, 3x, 'CONSISTS OF RESIDUE', i5, /)14(' GRP', i5, ' RES', i5, ' TO ', i5       )66(' ', 5x, '**** NUMBER OF FIND CARDS  = ', i5, 2x,               'IS TOO BIG ******', /)202(' ', 5x, 'GRAPH NAME  = ', a4, 2x,        'SYMBOL  = ', a2, 4x,               'TREE SYMBOL  = ', a1, 5x, 'RESIDUE TYPE  = ', a4, /)200(' ', 5x, 'ALL ATOMS THAT MEET 1 OF        THE FOLLOWING',           ' SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW', /)
                            ^
IOT Trap
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 6

So I am wondering whether the size of my system (400000) could also be the problem.
Need some help.
Thanks
Dadado

--- On Sun, 3/8/09, Ross Walker <ross_at_rosswalker.co.uk> wrote:
From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: [AMBER] PMEMD error message
To: "'AMBER Mailing List'" <amber_at_ambermd.org>
Date: Sunday, March 8, 2009, 4:52 PM

You are also missing a comma after nstlim=50000,dt=0.002

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Robert Duke
> Sent: Sunday, March 08, 2009 1:47 PM
> To: neville_forlemu_at_yahoo.com; AMBER Mailing List
> Subject: Re: [AMBER] PMEMD error message
>
> It's should be temp0, not tempO in the namelist (two places at least).
-
> Bob
> Duke
>
> ----- Original Message -----
> From: "neville forlemu" <neville_forlemu_at_yahoo.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Sunday, March 08, 2009 4:37 PM
> Subject: [AMBER] PMEMD error message
>
>
> Hello
>
> I get this error message, when I use the following command to heat up my
> system. It is complaining about a format error in my heat.in file. The
> file
> is shown below, has anyone had this problem and if yes what exactly in the
> file is it complaining. Thanks
>
>
> mpirun -np 4 /opt/brinsoft/amber8/exe/pmemd -O -i heat.in -o heat.out
> -p joxfact_wat.top -c joxfact_watmin.rst -r heat.rst -x heat.mdcrd -ref
> joxfact_watmin.rst
>
>
>
> lib-4324 : UNRECOVERABLE library error
>
>
>
>
>
> Encountered during a namelist READ from unit 5
>
> Fortran unit 5 is connected to a sequential formatted text file:
"heat.in"
>
> IOT Trap
>
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
>
> MPI: aborting job
>
> MPI: Received signal 6
>
>
>
>
> This is my heat.in file
> heating solvated joxfact complex
>
> &cntrl
>
> imin=0,irest=0,ntx=1,
>
> nstlim=50000,dt=0.002
>
> ntc=2,ntf=2,
>
> cut=12.0,ntb=1,
>
> ntpr=500,ntwx=500,
>
> ntt=3,gamma_ln=2.0,
>
> tempi=0.0,tempO=300.00,
>
> ntr=1,restraintmask=':1-50000',
>
> restraint_wt=2.0,
>
> nmropt=1
>
> /
>
> &wt TYPE='TEMPO',istep1=0,istep2=25000,
>
> value1=0.1,value2=300.0,/
>
> &wt TYPE='END'/
>
>
>
> Thanks
> Dadado
>
>
>
>
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